Is this the kind of dot probe design you're looking at? If so, then yes, DirectRT will do it no problem. If you are looking at any significant variation in design, let me know and I'll tell you DirectRT can accommodate.
Participants are asked to stare at a fixation cross on the center of the screen. Two stimuli appear randomly on either side of the screen. The stimuli are presented for a duration of 500ms before a dot is presented in the location where one of the stimuli was presented, at which point participants are instructed to respond on a remote key pad which side of the screen the dot appeared. Latency is measured. The fixation cross appears again for several seconds and then the cycle is repeated.